Bioinformatics

DISCOVERY NOTES:

Christian Weinel, Maria D. Ermolaeva, and Christos Ouzounis

PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1
Bioinformatics 2003 19: 1457-1460; doi:10.1093/bioinformatics/btg184 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

T. Z. DeSantis, I. Dubosarskiy, S. R. Murray, and G. L. Andersen

Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA
Bioinformatics 2003 19: 1461-1468; doi:10.1093/bioinformatics/btg200 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Dilip Rajagopalan

A comparison of statistical methods for analysis of high density oligonucleotide array data
Bioinformatics 2003 19: 1469-1476; doi:10.1093/bioinformatics/btg202 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Keith A. Baggerly, Li Deng, Jeffrey S. Morris, and C. Marcelo Aldaz

Differential expression in SAGE: accounting for normal between-library variation
Bioinformatics 2003 19: 1477-1483; doi:10.1093/bioinformatics/btg173 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R.L. Somorjai, B. Dolenko, and R. Baumgartner

Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions
Bioinformatics 2003 19: 1484-1491; doi:10.1093/bioinformatics/btg182 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ian Korf

Serial BLAST searching
Bioinformatics 2003 19: 1492-1496; doi:10.1093/bioinformatics/btg199 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Louxin Zhang, Bin Ma, Lusheng Wang, and Ying Xu

Greedy method for inferring tandem duplication history
Bioinformatics 2003 19: 1497-1504; doi:10.1093/bioinformatics/btg191 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ari Löytynoja and Michel C. Milinkovitch

A hidden Markov model for progressive multiple alignment
Bioinformatics 2003 19: 1505-1513; doi:10.1093/bioinformatics/btg193 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yoshiharu Hayashi, Katsuyoshi Sakaguchi, Mime Kobayashi, Masaki Kobayashi, Yo Kikuchi, and Eiichiro Ichiishi

Molecular evaluation using in silico protein interaction profiles
Bioinformatics 2003 19: 1514-1523; doi:10.1093/bioinformatics/btg189 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jie Wu, Simon Kasif, and Charles DeLisi

Identification of functional links between genes using phylogenetic profiles
Bioinformatics 2003 19: 1524-1530; doi:10.1093/bioinformatics/btg187 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David Mittelman, Ruslan Sadreyev, and Nick Grishin

Probabilistic scoring measures for profile–profile comparison yield more accurate short seed alignments
Bioinformatics 2003 19: 1531-1539; doi:10.1093/bioinformatics/btg185 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Bala Krishnamoorthy and Alexander Tropsha

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
Bioinformatics 2003 19: 1540-1548; doi:10.1093/bioinformatics/btg186 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Homayoun Valafar and James H. Prestegard

Rapid classification of a protein fold family using a statistical analysis of dipolar couplings
Bioinformatics 2003 19: 1549-1555; doi:10.1093/bioinformatics/btg201 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Simon Whelan, Paul I. W. de Bakker, and Nick Goldman

Pandit: a database of protein and associated nucleotide domains with inferred trees
Bioinformatics 2003 19: 1556-1563; doi:10.1093/bioinformatics/btg188 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Patrick Lambrix, Manal Habbouche, and Marta Pérez

Evaluation of ontology development tools for bioinformatics
Bioinformatics 2003 19: 1564-1571; doi:10.1093/bioinformatics/btg194 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Fredrik Ronquist and John P. Huelsenbeck

MrBayes 3: Bayesian phylogenetic inference under mixed models
Bioinformatics 2003 19: 1572-1574; doi:10.1093/bioinformatics/btg180 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, and Burkhard Morgenstern

AGenDA: homology-based gene prediction
Bioinformatics 2003 19: 1575-1577; doi:10.1093/bioinformatics/btg181 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yang Su, T.M. Murali, Vladimir Pavlovic, Michael Schaffer, and Simon Kasif

RankGene: identification of diagnostic genes based on expression data
Bioinformatics 2003 19: 1578-1579; doi:10.1093/bioinformatics/btg179 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

Sacha A. F. T. van Hijum, Anne de Jong, Girbe Buist, Jan Kok, and Oscar P. Kuipers

UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons
Bioinformatics 2003 19: 1580-1582; doi:10.1093/bioinformatics/btg203 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Naoki Sato and Shigeki Ehira

GenoMap, a circular genome data viewer
Bioinformatics 2003 19: 1583-1584; doi:10.1093/bioinformatics/btg195 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kuo-Bin Li

ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Bioinformatics 2003 19: 1585-1586; doi:10.1093/bioinformatics/btg192 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Apuã C. M. Paquola, Milton Y. Nishyiama, Jr, Eduardo M. Reis, Aline M. da Silva, and Sergio Verjovski-Almeida

ESTWeb: bioinformatics services for EST sequencing projects
Bioinformatics 2003 19: 1587-1588; doi:10.1093/bioinformatics/btg196 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Guoli Wang and Roland L. Dunbrack, Jr

PISCES: a protein sequence culling server
Bioinformatics 2003 19: 1589-1591; doi:10.1093/bioinformatics/btg224 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. Sammeth, J. Rothgänger, W. Esser, J. Albert, J. Stoye, and D. Harmsen

QAlign: quality-based multiple alignments with dynamic phylogenetic analysis
Bioinformatics 2003 19: 1592-1593; doi:10.1093/bioinformatics/btg197 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Stephen F. Madden, Barry O’Donovan, Simon J. Furney, Hugh R. Brady, Guenole Silvestre, and Peter P. Doran

Digital extractor: analysis of digital differential display output
Bioinformatics 2003 19: 1594-1595; doi:10.1093/bioinformatics/btg198 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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